Merge branch 'Tethys' of https://github.com/douggillespie/PAMGuard into Tethys

src/tethys/calibration/CalibrationHandler.java

@@ -45,9 +45,11 @@ import tethys.TethysTimeFuncs;
 import tethys.calibration.swing.CalibrationsExportWizard;
 import tethys.dbxml.DBXMLConnect;
 import tethys.dbxml.TethysException;
+import tethys.niluswraps.NilusChecker;
 import tethys.niluswraps.NilusSettingsWrapper;
 import tethys.niluswraps.NilusUnpacker;
 import tethys.pamdata.AutoTethysProvider;
+import tethys.reporter.TethysReporter;
 
 public class CalibrationHandler implements TethysStateObserver {
 
@@ -186,6 +188,7 @@ public class CalibrationHandler implements TethysStateObserver {
 		int nExport = 0;
 		boolean overwrite = false;
 		boolean exists;
+		TethysReporter.getTethysReporter().clear();
 		for (int i = 0; i < nPhone; i++) {
 //			String docName = getHydrophoneId(i);
 			NilusSettingsWrapper<Calibration> clonedWrap = wrappedSample.clone();
@@ -195,9 +198,20 @@ public class CalibrationHandler implements TethysStateObserver {
 				calDoc.setMetadataInfo(sampleCal.getMetadataInfo());				
 				calDoc.setProcess(sampleCal.getProcess());
 				calDoc.setQualityAssurance(sampleCal.getQualityAssurance());
+				if (NilusChecker.isEmpty(sampleCal.getResponsibleParty()) == false) {
 					calDoc.setResponsibleParty(sampleCal.getResponsibleParty());
+				}
 				calDoc.setTimeStamp(sampleCal.getTimeStamp());
 			}
+			// check the contact info in the metadata. 
+			// can't so because it's required. 
+//			MetadataInfo metaData = calDoc.getMetadataInfo();
+//			if (metaData != null) {
+//				if (NilusChecker.isEmpty(metaData.getContact())) {
+//					metaData.setContact(null);
+//				}
+//			}
+			
 			
 			addParameterDetails(calDoc, i);
 			
@@ -233,6 +247,7 @@ public class CalibrationHandler implements TethysStateObserver {
 			}
 		}
 		tethysControl.sendStateUpdate(new TethysState(TethysState.StateType.EXPORTRDATA, Collection.Calibrations));
+		TethysReporter.getTethysReporter().showReport(true);
 		return nExport;
 	}
 	
@@ -405,6 +420,10 @@ public class CalibrationHandler implements TethysStateObserver {
 		hz.add(Double.valueOf(0));
 		db.add(Double.valueOf(hSens+preampGain));
 		
+		if (NilusChecker.isEmpty(calibration.getResponsibleParty())) {
+			calibration.setResponsibleParty(null);
+		}
+		
 		MetadataInfo metaInf = calibration.getMetadataInfo();
 		if (metaInf == null) {
 			metaInf = new MetadataInfo();
@@ -417,6 +436,12 @@ public class CalibrationHandler implements TethysStateObserver {
 			contact = new ResponsibleParty();
 			metaInf.setContact(contact);
 		}
+		if (NilusChecker.isEmpty(metaInf.getContact())) {
+			metaInf.setContact(null);
+		}
+		if (NilusChecker.isEmpty(metaInf)) {
+			calibration.setMetadataInfo(null);
+		}
 		contact.setIndividualName("Unknown");
 		contact.setOrganizationName("unknown");
 		

src/tethys/dbxml/DBXMLConnect.java

@@ -23,6 +23,8 @@ import tethys.TethysControl;
 import tethys.database.TethysActions;
 import tethys.database.TethysLogger;
 import tethys.output.TethysExportParams;
+import tethys.reporter.TethysReport;
+import tethys.reporter.TethysReporter;
 
 /**
  * Class containing functions for managing the database connection. Opening, closing,
@@ -207,6 +209,8 @@ public class DBXMLConnect {
 		 */
 		boolean error = importReturn.contains("<Error");
 		boolean success = importReturn.contains("<Success>");
+		String name = tempFile.getName();
+		TethysReporter.getTethysReporter().addReport(new TethysReport(success, collection, name, name));
 //		error = !success; might be a better options. 
 		if (error) {
 			throw new TethysException("Error posting to Tethys", importReturn);

src/tethys/deployment/DeploymentHandler.java

@@ -84,6 +84,7 @@ import tethys.deployment.swing.RecordingGapDialog;
 import tethys.niluswraps.PDeployment;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.AutoTethysProvider;
+import tethys.reporter.TethysReporter;
 import tethys.swing.DeploymentTableObserver;
 
 /**
@@ -387,12 +388,14 @@ public class DeploymentHandler implements TethysStateObserver, DeploymentTableOb
 	 * @param selectedDeployments
 	 */
 	public void exportDeployments(ArrayList<RecordingPeriod> selectedDeployments) {
+		TethysReporter.getTethysReporter().clear();
 		if (deploymentExportOptions.separateDeployments) {
 			exportSeparateDeployments(selectedDeployments);
 		}
 		else {
 			exportOneDeploymnet(selectedDeployments);
 		}
+		TethysReporter.getTethysReporter().showReport(tethysControl.getGuiFrame(), true);
 	}
 	
 	/**

src/tethys/detection/DetectionsHandler.java

@@ -43,6 +43,7 @@ import tethys.output.DatablockSynchInfo;
 import tethys.output.StreamExportParams;
 import tethys.output.TethysExportParams;
 import tethys.pamdata.TethysDataProvider;
+import tethys.reporter.TethysReporter;
 import tethys.species.DataBlockSpeciesManager;
 import tethys.swing.export.DetectionsExportWizard;
 
@@ -587,6 +588,7 @@ public class DetectionsHandler {
 			this.dataBlock = dataBlock;
 			this.exportParams = exportParams;
 			this.exportObserver = exportObserver;
+			TethysReporter.getTethysReporter().clear();
 		}
 
 		public void publish(DetectionExportProgress exportProgress) {
@@ -617,6 +619,7 @@ public class DetectionsHandler {
 			DetectionExportProgress prog = new DetectionExportProgress(null, null, 0, 0, 0, 0, DetectionExportProgress.STATE_COMPLETE);
 			tethysControl.exportedDetections(dataBlock);
 			exportObserver.update(prog);
+			TethysReporter.getTethysReporter().showReport(tethysControl.getGuiFrame(), true);
 		}
 
 		@Override

src/tethys/niluswraps/NilusChecker.java

@@ -0,0 +1,75 @@
+package tethys.niluswraps;
+
+import java.lang.reflect.InvocationTargetException;
+import java.lang.reflect.Method;
+import java.util.List;
+
+import nilus.ResponsibleParty;
+
+/**
+ * A few static checks of some nilus classes to see if it's 
+ * worth writing them or not. 
+ * @author dg50
+ *
+ */
+public class NilusChecker {
+
+	public static boolean isEmpty(Object nilusObject) {
+		boolean empty = true;
+		if (nilusObject == null) {
+			return true;
+		}
+		// and check all getters 
+		Class<? extends Object> nilusClass = nilusObject.getClass();
+		Method[] methods = nilusClass.getDeclaredMethods();
+		// searching for getters. 
+		int nGet = 0;
+		for (int i = 0; i < methods.length; i++) {
+			Method method = methods[i];
+			if (method.getName().startsWith("get") && method.getParameterCount() == 0) {
+				nGet ++;
+				try {
+					Object got = method.invoke(nilusObject, null);
+					if (got != null) {
+						if (got instanceof String) {
+							if (isEmptyString((String) got) == false) {
+								empty = false;
+							}
+						}
+						else if (got instanceof List<?>) {
+							if (isEmptyList((List) got) == false) {
+								empty = false;
+							}
+						}
+						else if (isEmpty(got) == false) {// it's some other class type, so recurecively ask back here.
+							empty = false;
+						}
+						
+					}
+				} catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+					return false; // better save than sorry if we don't understand. 
+				}
+			}
+		}
+		if (nGet == 0) {
+			// there weren't any understandable getters, so assume not empty. May be some other primitive type. 
+			empty = false;
+		}
+			
+		return empty;
+	}
+	
+	private static boolean isEmptyList(List got) {
+		if (got == null) {
+			return true;
+		}
+		return got.size() == 0;
+	}
+
+	public static boolean isEmptyString(String string) {
+		if (string == null || string.length() == 0) {
+			return true;
+		}
+		return false;
+	}
+}

src/tethys/reporter/TethysReport.java

@@ -0,0 +1,56 @@
+package tethys.reporter;
+
+import tethys.Collection;
+
+public class TethysReport {
+
+	private boolean success;
+	
+	private Collection collection;
+	 
+	private String docName;
+	
+	private String docId;
+
+	/**
+	 * @param success
+	 * @param collection
+	 * @param docName
+	 * @param docId
+	 */
+	public TethysReport(boolean success, Collection collection, String docName, String docId) {
+		this.success = success;
+		this.collection = collection;
+		this.docName = docName;
+		this.docId = docId;
+	}
+
+	/**
+	 * @return the success
+	 */
+	public boolean isSuccess() {
+		return success;
+	}
+
+	/**
+	 * @return the collection
+	 */
+	public Collection getCollection() {
+		return collection;
+	}
+
+	/**
+	 * @return the docName
+	 */
+	public String getDocName() {
+		return docName;
+	}
+
+	/**
+	 * @return the docId
+	 */
+	public String getDocId() {
+		return docId;
+	}
+	
+}

src/tethys/reporter/TethysReporter.java

@@ -0,0 +1,118 @@
+package tethys.reporter;
+
+import java.awt.Window;
+import java.util.ArrayList;
+
+import PamController.PamController;
+import PamView.dialog.warn.WarnOnce;
+
+/**
+ * Set of functions to provide mesage reports on Tethys output. This 
+ * will work with the existing WarnOnce type pop-up, the primary purpose
+ * of the functions here being to collate information, possibly from 
+ * several document writes, before issuing an overall report. 
+ * @author dg50
+ *
+ */
+public class TethysReporter {
+
+	private static TethysReporter singleInstance;
+	
+	private ArrayList<TethysReport> tethysReports;
+
+	private TethysReporter() {
+		tethysReports = new ArrayList<TethysReport>();
+	}
+	
+	/**
+	 * Get the reporter. 
+	 * @return
+	 */
+	public static final TethysReporter getTethysReporter() {
+		if (singleInstance == null) {
+			singleInstance = new TethysReporter();
+		}
+		return singleInstance;
+	}
+	
+	/**
+	 * Clear all reports
+	 */
+	synchronized public void clear() {
+		tethysReports.clear();
+	}
+	
+	/**
+	 * Add a report after attempting to write a document
+	 * @param report
+	 */
+	synchronized public void addReport(TethysReport report) {
+		tethysReports.add(report);
+	}
+	
+	/**
+	 * Get the current number of reports
+	 * @return number of reports
+	 */
+	synchronized public int getSize() {
+		return tethysReports.size();
+	}
+	
+	/**
+	 * Get a summary string of all reported writes using html to separate each ont a separat eline
+	 * @return
+	 */
+	synchronized public String getReportString() {
+		if (tethysReports.size() == 0) {
+			return "No reports";
+		}
+		String str = "<html>";
+		for (int i = 0; i < tethysReports.size(); i++) {
+			TethysReport aReport = tethysReports.get(i);
+			String res = aReport.isSuccess() ? "Success" : "Failure";
+			if (i > 0) {
+				str += "<br>";
+			}
+		    str += String.format("%s writing %s document %s to Tethys", res, aReport.getCollection().collectionName(), aReport.getDocName());	
+		}
+		
+		
+		str += "</html>";
+		return str;
+	}
+	
+	/**
+	 * Get a count of failed document writes
+	 * @return failure count
+	 */
+	public int countFails() {
+		int fails = 0;
+		for (TethysReport aReport : tethysReports) {
+			if (aReport.isSuccess() == false) {
+				fails++;
+			}
+		}
+		return fails;
+	}
+
+	/**
+	 * Show a report in a popup window
+	 * @param clear clear the list of reports afterwards
+	 */
+	public void showReport(boolean clear) {
+		showReport(PamController.getMainFrame(), clear);
+	}
+	
+	/**
+	 * Show a report on a popup window
+	 * @param window parent frame
+	 * @param clear clear the list of reports afterwards
+	 */
+	public void showReport(Window window, boolean clear) {
+		boolean probs = countFails() > 0;
+		WarnOnce.showNamedWarning("TethysReporter", window, "Tethys Document Writer", getReportString(), WarnOnce.WARNING_MESSAGE);
+		if (clear) {
+			clear();
+		}
+	}
+}